ArticleProceedings of the National Academy of Sciences of the United States of America2011
Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
108 citing papers in PubMed.
- Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- The Marchantia polymorpha pangenome reveals ancient mechanisms of plant adaptation to the environment.Nature genetics · 2025Article
- Antagonism within mutualism: host control of symbionts through nodule-specific antimicrobial peptides.Frontiers in microbiology · 2025Review
- Genomic selection for agronomical phenotypes using genome-wide SNPs and SVs in pearl millet.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Previously unmeasured genetic diversity explains part of Lewontin's paradox in abioRxiv : the preprint server for biology · 2024Article
- Analyzing Medicago spp. seed morphology using GWAS and machine learning.Scientific reports · 2024Article
- A genome-wide study of the lipoxygenase gene families in Medicago truncatula and Medicago sativa reveals that MtLOX24 participates in the methyl jasmonate response.BMC genomics · 2024Article
- First Insights into Population Structure and Genetic Diversity Versus Host Specificity in Trypanorhynch Tapeworms Using Multiplexed Shotgun Genotyping.Genome biology and evolution · 2023Article
- Association mapping in bambara groundnut [Vigna subterranea (L.) Verdc.] reveals loci associated with agro-morphological traits.BMC genomics · 2023Article
- Chromosome-scale assembly and analysis of Melilotus officinalis genome for SSR development and nodulation genes analysis.The plant genome · 2023Article
- Review
- Article
- Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly AsexualInternational journal of molecular sciences · 2023Article
- Article
- Article
- Plastid phylogenomics uncovers multiple species in Medicago truncatula (Fabaceae) germplasm accessions.Scientific reports · 2022Article
- Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides.Journal of experimental botany · 2022Article
- Comparison of structural variants in the whole genome sequences of two Medicago truncatula ecotypes: Jemalong A17 and R108.BMC plant biology · 2022Article
- The Genomic Signature of Allopatric Speciation in a Songbird Is Shaped by Genome Architecture (Aves: Certhia americana).Genome biology and evolution · 2021Article
48 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Medicago truncatula is a model for investigating legume genetics, including the genetics and evolution of legume-rhizobia symbiosis. We used whole-genome sequence data to identify and characterize sequence polymorphisms and linkage disequilibrium (LD) in a diverse collection of 26 M. truncatula accessions. Our analyses reveal that M. truncatula harbors both higher diversity and less LD than soybean (Glycine max) and exhibits patterns of LD and recombination similar to Arabidopsis thaliana. The population-scaled recombination rate is approximately one-third of the mutation rate, consistent with expectations for a species with a high selfing rate. Linkage disequilibrium, however, is not extensive, and therefore, the low recombination rate is likely not a major constraint to adaptation. Nucleotide diversity in 100-kb windows was negatively correlated with gene density, which is expected if diversity is shaped by selection acting against slightly deleterious mutations. Among putative coding regions, members of four gene families harbor significantly higher diversity than the genome-wide average. Three of these families are involved in resistance against pathogens; one of these families, the nodule-specific, cysteine-rich gene family, is specific to the galegoid legumes and is involved in control of rhizobial differentiation. The more than 3 million SNPs that we detected, approximately one-half of which are present in more than one accession, are a valuable resource for genome-wide association mapping of genes responsible for phenotypic diversity in legumes, especially traits associated with symbiosis and nodulation.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.